Stress Knowledge Map:A knowledge graph resource for systems biology analysis of plant stress responses  

作　　者：Carissa Bleker Ziva Ramsak Andras Bittner Vid Podpecan Maja Zagorscak Bernhard Wurzinger Spela Baebler Marko Petek Maja Kriznik Annelotte van Dieren Juliane Gruber Leila Afjehi-Sadat Wolfram Weckwerth Anze Zupanic Markus Teige Ute CVothknecht Kristina Gruden 

机构地区：[1]Department of Biotechnology and Systems Biology,National Institute of Biology,Vecna pot 121,1000 Ljubljana,Slovenia [2]Plant Cell Biology,Institute of Cellular and Molecular Botany,University of Bonn,Kirschallee 1,53115 Bonn,Germany [3]Department of Knowledge Technologies,Jozef Stefan Institute,Jamova cesta 39,1000 Ljubljana,Slovenia [4]Department of Functional&Evolutionary Ecology,University of Vienna,Djerassiplatz 1,1030 Vienna,Austria [5]Mass Spectrometry Unit,Core Facility Shared Services,University of Vienna,Djerassiplatz 1,1030 Vienna,Austria

出　　处：《Plant Communications》2024年第6期17-31,共15页植物通讯（英文）

基　　金：funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement 862858(ADAPT);the Slovenian Research Agency under grant agreements 1000-15-0105,Z7-1888,J4-1777,P4-0165,N4-0199,Z4-50146,and J4-3089;ELIXIR,the research infrastructure for life science data through the ELIXIR Implementation Study“Increasing plant data findability for ELIXIR and beyond”and ELIXIR-SI.We gratefully acknowledge funding from the Deutsche Forschungsgemeinschaft(DFG)to U.C.V.(INST 217/939-1 FUGG).

摘　　要：Stress Knowledge Map(SKM;https://skm.nib.si)is a publicly available resource containing two complementary knowledge graphs that describe the current knowledge of biochemical,signaling,and regulatory molecular interactions in plants:a highly curated model of plant stress signaling(PSS;543 reactions)and a large comprehensive knowledge network(488390 interactions).Both were constructed by domain experts through systematic curation of diverse literature and database resources.SKM provides a single entry point for investigations of plant stress response and related growth trade-offs,as well as interactive explorations of current knowledge.PSS is also formulated as a qualitative and quantitative model for systems biology and thus represents a starting point for a plant digital twin.Here,we describe the features of SKM and show,through two case studies,how it can be used for complex analyses,including systematic hypothesis generation and design of validation experiments,or to gain new insights into experimental observations in plant biology.

关 键 词：knowledge graph plant stress responses plant signaling systems biology plant digital twin 

分 类 号：Q94[生物学—植物学]